BioMuta Pipeline information

[jeet-vora]

The plan for updating the BioMuta pipeline was to be given to EBI for them to generate the datasets. We are still in talks with them but the most important issue is the disease and clinical patient data that they do not have. For now we will re-work in the BioMuta pipeline to generate datasets

Also they are in talks with COSMIC to share the data with us and also are looking into TCGA data.

We will forget ICGC and CIViC datasets will be coming from Karen

The slides created for EBI will explain the current BioMuta pipeline.

[mariacuria]

1. TCGA: look for current datasets and see if they're the same as before. Compare with current data on the GlyGen server.
   • Blocker: waiting for Google Cloud access
2. COSMIC has license restrictions?
   • For non-commercial use, you don't need to pay for a COSMIC license.
   • Students and employees of institutions using COSMIC for non-commercial purposes may download all COSMIC data for free after registering with their institutional email address. I have registered.

[mariacuria]

TCGA

1. Open-access data status: waiting for credit card information required to use Google Cloud
2. Restricted data (dbGaP) status: waiting for the eRA Commons account to log in on dbGaP

[mariacuria]

dbGaP UPD status: eRA Commons account has been set up, waiting for instructions on how to use the keys from our eRA account admin

[mariacuria]

dbGaP UPD status: got access. Will upd instructions on Sharepoint and the wiki.

[jeet-vora]

@mariacuria

Raja mentioned that we can get COSMIC data from EBI and he is ok if the data is without disease information as we had it earlier. We can contact James to see when he can provide the data to us.

[mariacuria]

UPD: scrap the idea of getting COSMIC data from EBI. Looking whether it is included on cBioPortal.

[mariacuria]

UPD: cBioPortal --> BioMuta pipeline has the following standard BioMuta columns:

• sample_name
• chr_id
• start_pos (needs liftover)
• end_pos (needs liftover)
• ref_nt
• alt_nt
• aa_pos
• ref_aa
• alt_aa
• do_name (note to self: https://disease-ontology.org/do)
• source

The following columns are in the works:

• unitprot_canonical_ac
• dbsnp_id